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Curriculum Vitae Curriculum Vitae Tandy Warnow Grainger Distinguished Chair in Engineering 1 Contact Information Department of Computer Science The University of Illinois at Urbana-Champaign Email: [email protected] Homepage: http://tandy.cs.illinois.edu 2 Research Interests Phylogenetic tree inference in biology and historical linguistics, multiple sequence alignment, metage- nomic analysis, big data, statistical inference, probabilistic analysis of algorithms, machine learning, combinatorial and graph-theoretic algorithms, and experimental performance studies of algorithms. 3 Professional Appointments • Co-chief scientist, C3.ai Digital Transformation Institute, 2020-present • Grainger Distinguished Chair in Engineering, 2020-present • Associate Head for Computer Science, 2019-present • Special advisor to the Head of the Department of Computer Science, 2016-present • Associate Head for the Department of Computer Science, 2017-2018. • Founder Professor of Computer Science, the University of Illinois at Urbana-Champaign, 2014- 2019 • Member, Carl R. Woese Institute for Genomic Biology. Affiliate of the National Center for Supercomputing Applications (NCSA), Coordinated Sciences Laboratory, and the Unit for Criticism and Interpretive Theory. Affiliate faculty member in the Departments of Mathe- matics, Electrical and Computer Engineering, Bioengineering, Statistics, Entomology, Plant Biology, and Evolution, Ecology, and Behavior, 2014-present. • National Science Foundation, Program Director for Big Data, July 2012-July 2013. • Member, Big Data Senior Steering Group of NITRD (The Networking and Information Tech- nology Research and Development Program), subcomittee of the National Technology Council (coordinating federal agencies), 2012-2013 • Departmental Scholar, Institute for Pure and Applied Mathematics, UCLA, Fall 2011 • Visiting Researcher, University of Maryland, Spring and Summer 2011. 1 • Visiting Researcher, Smithsonian Institute, Spring and Summer 2011. • Professeur Invit´e,Ecole Polytechnique F´ed´erale de Lausanne (EPFL), Summer 2010. • Visiting Researcher, Microsoft New England, Fall 2010. • Visiting Scholar, UC Berkeley, Summer 2009; co-taught (with Johanna Nichols and Donald Ringe) the course Computational Methods in Linguistic Reconstruction at the 2009 Linguistic Institute held at Berkeley. • Visiting Scholar, Program for Evolutionary Dynamics at Harvard University, 2004-2005. • Radcliffe Institute for Advanced Studies, Emeline Bigelow Conland Fellow, 2003-2004. • Visiting Scholar, University of California at Berkeley, 2002-2004. • University of Texas at Austin, 9/1999 - 2014 { Co-Director, Center for Computational Biology and Bioinformatics, 2001-2003 { Professor, Department of Computer Science, University of Texas at Austin (effective 9/1/2003). Assoc. Professor 9/1999-9/2003. { Member, Texas Institute for Computational and Applied Mathematics, and the Institute for Cellular and Molecular Biology. { Member, Graduate Programs in Computer Sciences, Molecular Biology, Computational and Applied Mathematics, and the Program in Ecology, Evolution, and Behavior. • University of Pennsylvania, 9/1993-8/1999. { Associate Professor (tenured January 1998), Department of Computer and Information Sciences. { Member, Institute for Research in Cognitive Sciences. { Co-PI, Graduate and Postdoctoral Research Training Program (RTG) in Computational Biology. (PI: Warren Ewens). • University of Arizona, 9/1998-8/1999, Visiting Professor, Departments of Computer Science and Ecology and Evolutionary Biology. • Yale University, 1997-1998, Visiting Researcher, Department of Computer Science. • Princeton University, 1997-1998, Visiting Professor, Departments of Mathematics and Com- puter Sciences. • DIMACS, 1996, visitor. 4 Education • Postdoctoral Fellowship (1991-1992), University of Southern California, with Michael Water- man and Simon Tavar´e. • Ph.D. Mathematics (1991), University of California, Berkeley. Dissertation: Combinatorial Algorithms for Constructing Phylogenetic Trees. Committee: Eugene Lawler (advisor), Manuel Blum, David Gale, Dan Gusfield, and Richard Karp. • B.A. Mathematics (1984), magna cum lauda, University of California, Berkeley. 2 5 Honors • Language (Journal of the Linguistic Society of America), included one of my papers (Nakhleh, Ringe, and Warnow, `Perfect Phylogenetic Networks: A new methodology for reconstructing the evolutionary history of natural languages, " Language (Journal of the Linguistic Society of America), 81(2), pp. 382-420, June 2005) in their selection of top 20 papers from the last 30 years (see https://www.linguisticsociety.org/content/best-language-volume-iii) • Teaching: I have been included in the List of Teachers Rated Excellent by their students four times (Spring 2017 for CS 466 and CS 581, Spring 2018 for CS 581, and Fall 2020 for CS 581). In the last of these, I was listed as \Outstanding". • Elected member, Electorate Nominating Committee (ENC) of the Section on Information, Computing, & Communication, American Association for the Advancement of Science (AAAS), 2019-present • Fellow of the International Society for Computational Biology (ISCB), 2017. • Fellow of the Association for Computing Machinery (ACM), 2015. Citation: For contributions to mathematical theory, algorithms, and software for large-scale molecular phylogenetics and historical linguistics. • Founder Professor of Engineering, the University of Illinois at Urbana-Champaign, 2014- present • David Bruton, Jr. Centennial Professorship in Computer Science, 2010 - 2014 • John Simon Guggenheim Foundation Fellowship, 2011, New problems in evolutionary estima- tion. • Radcliffe Institute for Advanced Study, Emeline Bigelow Conland Fellow, 2003-2004. • David and Lucile Packard Foundation Fellowship, 1996-2001, Algorithms for reconstructing evolutionary trees in biology and linguistics. • NSF National Young Investigator Award, 1994-99. Combinatorial Problems in Evolutionary Tree Construction. 6 Current and Former Graduate Students Current: • Gillian Chu (MS student, degree expected 2022) • Baqiao Liu (PhD student, degree expected 2026) • Minhyuk Park (PhD student, degree expected 2025) • Chengze Shen (PhD student, degree expected 2025) • Yasamin Tabatabaee (PhD student, degree expected 2026) • Eleanor Wedell (MS student, degree expected 2022) • James Willson (PhD student, degree expected 2026) 3 Former: • Md. Shamsuzzoha Bayzid (PhD Fall 2016). Associate Professor, Department of Computer Science and Engineering (CSE), Bangladesh University of Engineering and Technology. • Sarah Christensen (PhD student in Computer Science, co-advised with Mohammed El-Kebir), PhD 2020. Now working in industry • Ganesh Ganapathy (PhD August 2006), Apple Computers • Ashu Gupta (MS May 2016, Computer Science at the University of Illinois at Urbana-Champaign), now at Apple • Kevin Liu (PhD May 2011), Assistant Professor of Computer Science, Michigan State Univer- sity • Siavash Mirarab (PhD August 2015), Associate Professor of Electrical and Computer Engi- neering, UCSD • Erin Molloy (PhD August 2020), Assistant Professor of Computer Science, Univ Maryland starting 2021. Co-advised with Bill Gropp, PhD August 2020) • Luay Nakhleh (PhD May 2004), Dean of Engineering and Professor of Computer Science at Rice University. • Serita Nelesen (PhD December 2009), Software developer for Neural Planet • Nam-phuong Nguyen (PhD August 2014), Principle Scientist, Bioinformatics, Boundless Bio • Michael Nute (PhD student 2019), postdoctoral researcher at Rice University • Usman Roshan (PhD May 2004), Associate Professor of Computer Science at NJIT. • Vladimir Smirnov (PhD, August 2021), now postdoctoral researcher • Michelle (Shel) Swenson (PhD May 2009), Lecturer, Department of Mathematics, University of Tennessee at Knoxville • Pranjal Vachaspati (PhD December 2019), now Software Engineer at Google • Li-San Wang (PhD May 2003), Professor of Pathology and Laboratory Medicine at the Uni- versity of Pennsylvania. • Shibu Yooseph (PhD received 2000), Professor of Computer Science at Central Florida Uni- versity • Xilin Yu (MS awarded 2019), now software engineer at Amazon 7 Current and Former Postdoctoral advisees Current: • Paul Zaharias, Feb 2020-present Former: • Kevin Atteson (Chief Quant at Summer Road) 4 • Fran¸cois Barban¸con(now self-employed) • Ruth Davidson (NSF Postdoctoral Fellow in Mathematics, now J.L. Doob Research Assistant Professor in the Department of Mathematics at UIUC) • Dannie Durand (Associate Professor of Biology and of Computer Science, Carnegie Mellon University) • Daniel Huson (C4 Professor of Bioinformatics, Tubingen University, Germany) • Nam-phuong Nguyen (now Principle Scientist, Bioinformatics, Boundless BIO) • Ken Rice (now retired) • Katherine St. John (Professor of Computer Science, Hunter College, CUNY) • Elizabeth Sweedyk (Associate Professor of Computer Science, Harvey Mudd College) • Shel Swenson (Lecturer, University of Tennessee at Knoxville, Mathematics Department) 8 Current Grant Support • National Science Foundation (NSF) 2006069, IIBR Informatics: Advancing Bioinformatics Methods using Ensembles of Profile Hidden Markov Models. PI Warnow (Co-PI: Jian Peng), August 15, 2020 to August 14, 2023. This project will extend the theory foundations of ensembles of profile HMMs, and use them for protein structure and function prediction. 9 Recent Grant Support • National Science Foundation (NSF) DBI:1458652. ABI Innovation: New methods for multiple sequence alignment with improved accuracy and scalability. PI Warnow. August 15, 2015 to July
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